In 1991, he became a professor at the Biocenter of the University of Würzburg, where he now serves as head of the Department of Physiological Chemistry. He is a founder of the biomedicine program at Würzburg.

For the last thirty-five years, Schartl has studied the molecular genetics and biochemistry of cancer, in particular malignant melanoma. He has also explored the mechanisms that guide the molecular-developmental decisions in embryos to become male or female. Both topics are linked by common molecular and developmental methods and by the evolutionary and comparative approach to using fish as models for understanding human physiology and diseases.

Schartl is vice chairman of the Rudolf Virchow Center, which is the university’s research center for experimental medicine. He is an adjunct professor for experimental cancer research in the Department of Molecular Biology at the University of Bergen in Norway. He has chaired the scientific advisory board for the Center of Molecular Biology at the University of Göttingen since 2005 and for the Sars Centre for Molecular Marine Biology in Bergen since 1999.

He is member of the Leopoldina, the National Academy of Sciences of Germany.

Honors include the Heisenberg Award from the German Research Foundation and the Jenkinson Lecture of the Oxford University in 1991 and the NUSS Annual Lecturer and Guest Professorship at National University of Singapore and the Ray Chaudhuri Lecture at the University of Varanasi in India in 2011. He received an honorary doctoral degree from the University of Bergen in 2004 and Japan’s Prince Hitachi Prize for Comparative Oncology in 2007.

He served as president of the German Genetics Society in 2009-11 and has served as a member of its advisory board since 1999.

In 2016 he became Fellow of the Texas Institute of Advanced Study at Texas A&M and is a visiting professor at the Department of Biology.